I've had good luck talking to the station master and the police first in the NJ Transit station (Hoboken Trerminal). NJ Transit now has a policy specifically allowing photography in public areas of their stations, but the tripods seem to be at the NJ Transit Police' discretion.
PATH is a whole other world. I once went and got a permit from them but the hassle wasn't worth it to me to ever do again.
In NYC, if I'm planning to be in an area that's like to have ANY real crowd I'll file for the free permit. I've only been "hassled" twice and both times had a permit. The cops were very polite. Often times cops are interested and stop and ask if they can take a look at the ground glass.
I have been hassled in the NYC subway (never even tried a tripod, as I knew they were verboten), but a polite discussion has usually resolved the matter. I've only lost the battle twice, when I didn't have time to really make an issue of it.
My advice, if you can, get a permit and get it with fairly general locations. It's free, anyway. And if you're in a "grey" area, politely let any police, etc. know what you are doing. Don't ask them, as this opens the door for them to say "no." Just say, "I just wanted to let you know I'm going to be photographing blah blah blah. It's non-commercial. Just a hobby, etc."
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